How to save multiple baked textures?
Switch to Texture Paint mode and use the Save All Images button.  It will save any images that have been altered so long as they have already been previously saved.



Normally, I make sure everything is savable by preparing the textures in the folder on the hard-drive and then drag and drop them into the materials. This is quick and Blender will have a location to save them to when you use the image save button.